If you have been playing for a while, your Token inventory is overflowing with build tokens for early post-research and post-campaign hulls. Punishers, Citadels, Monoliths, Cannoneers, Skyfires, and other ships that are good to get a start with, but are now apparently worthless junk. After the defense rework, some of these are now anything but junk.
I'm starting with the Punisher because it is the one you are most likely to have a very large surplus of build tokens for. After the defense rework, it is also one of the most useful. It has a decent amount of base Armor and many weapon slots. It is also rated at tier 4.5, and since it is the ship everyone starts building up on, is very unlikely to be barred from common targets such as FMs no matter what target type they switch them to.
It is a Siege hull, so we'll start with a build designed to hit Siege targets. This build is identical to what many players were running with prior to the defense rework.
With 830K base Armor, adding Armor points to this hull is a waste. The best armor to use for Siege on this hull (and most other Siege hulls too) is the ballistic/radioactive combination charged armor. We don't care that much about its Charged Armor point pool, we are more interested in the dual Survival stats. It is also currently the only Charged armor that is NOT a Limited. After filling all 3 armor slots with this and adding Alloy Armor CL-4 special, we have about 195% Survival. This gives us a bit more than 1.6 million vs Siege damage types (not including Turret resistance which I'll cover in a bit), but don't forget the Charged Armor Pool. It acts as its own armor system within itself so Survival doesn't count. You just tack the total armor pool onto the end of your calculated total. In this case you get 190K of each damage type for a total armor vs. Siege class targets of about 1.8 million. THEN you add in the turret defense for Siege Battery or whatever other Turret defense bonus special. Siege Battery IV gives a nice 45%, so vs. Turret damage (which virtually all Siege damage is anyway) that adds another 810K for around 2.6 million. This sounds pretty good, but Siege targets do a lot more damage than other types. Defensively, this hull won't hold up in the higher targets, it is best used in much smaller ones. The only good thing here is the 190K of Charged Armor pool will cook off first, so this extends the instant repair for free time beyond what the Armor and Survival offer. The armor ratio works out to be about 495, times 300 seconds for 5m is 148K + the 190K from the charged armor for a total of 238K damage you can take for free and instant repair. As for offense, cannons are the best choice since they work well in Siege and the Punisher already has bonuses for them. You can fit 2 Devastators on after your engines, Cannon System IV, SIege Targeting, etc. That is plenty of damage for small Siege targets.
Punisher, the new Zelos?
The Punisher can be used in Garrison targets such as the current FM (soon to change to Assault though) with mediocre effect. Offensively it is in a bind because Garrison targets are most vulnerable to Explosive damage. Mortars do some OK damage but take too long to get to the target. Rockets need a range boost from the hull stats which the Punisher does not have. The offense in big Garrison targets really needs to come from a rocket ship like Icebreakers or Inferno Dragons that can flatten whole platforms very quickly while staying just out of range of the nastier guns.
Defensively the Punisher can fare a lot better, but what is defense without offensive capability? It's support, that's what it is. The Punisher can excel as a countermeasure support ship. Just before the defense rework, I would use a couple Zelos along with my Icebreakers in lvl 111 Research Garrison FM targets. They would shoot down missiles, mortars, and even some rockets, saving the whole fleet a lot of damage. Now the Zelos doesn't hold up very well at all like it used to. The Punisher doesn't have the built in countermeasure or accuracy bonus that the Zelos does, but will now take a lot more of a pounding than the Zelos if outfitted for it and still provide good countermeasure coverage.
Start by putting on two tiny explosive armors such as D1-X, and one tiny missile armor like D1-M, then a dual Missile/Explosive armor special such as MX-3. Your survival for both should be around 100%. You are going to be a bit shorter on the Explosive Survival side, so I like to use the Explosive Resistor engine instead of a normal one. Add Frontline Countermeasure for Turret defense and countermeasure upgrades. This gives a nice Turret defense of 45%. Not all of the damage from Garrison targets is from Turrets, but most of it is. You don't need to bother using the Limited countermeasures, it is expensive to collect enough to outfit whole ships with and their benefit is marginal. You can use standard Phalanx and Hails, but use the IVs to get the maximum accuracy and survival bonuses, you'll need both. 3 Phalanx 4s, 2 Hailstorm IVs, and 4 Sprint Countermeasures (these shoot down rockets) are a nice mix. You'll notice I left a weapon slot open, put a weapon here to set range when you target using the whole fleet or when it is on Auto. If you want this ship to hang out in back (advisable) then put on a really long range weapon such as a Squall Launcher. If you want it just in front (don't do this in Garrison targets) put a shorter range mortar such as a Pandemonium on it.
This will give you a countermeasure support ship that can take twice the pounding the Zelos can, and repairs in 1hr36m compared to 4hrs for the Zelos. You also get free build time at a much faster rate if you don't already have several months worth of Punisher tokens kicking around. VXP is also in huge supply compared to none for the Zelos. One or two of these mixed in with your Icebreakers will save the entire fleet repair time. The build can be adjusted for other target types as well, but countermeasures do best in Garrison targets because most of the weapons being fired at you can be taken out with countermeasures.
The Punisher can do surprisingly well in Assault targets (that will allow it in...) due to its high base Armor and lower repair time compared to Assault hulls. I currently have a couple tag along with Manticores to open titanium fleets. The Puns repair in less time than the Manticores for the same damage taken.
Start by adding two tiny corrosive armors such as the D2-CO and one missile armor like the D1-M, then the Alloy COM armor special. This will bring you to a bit over 100% Survival for Penetrating, but a bit less for Corrosive. After the addition of 5 Stinger missiles and their Survival bonus, this evens out. You now have an armor ratio better than the Manticore. You can complete the build with Speed System, Missile System, Carbon Fiber Casings and one other special. I prefer Agility System but if the platforms in Assault targets are giving you more of a problem then Siege Battery might work better both offensively and defensively. You can also ditch one Stinger, use Frontline Countermeasure, and add some Phalanx II's to cut down on the missile damage. A corrosive build is possible too. You can fit six Pantera Scatterguns on and swap the Guided Missile System for a Corrosive special. I prefer Narrowed Firing Aperture.